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Yorodumi- PDB-1lwl: Crystal Structure of Cytochrome P450-cam with a Fluorescent Probe... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1lwl | ||||||
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Title | Crystal Structure of Cytochrome P450-cam with a Fluorescent Probe D-8-Ad (Adamantane-1-carboxylic acid-5-dimethylamino-naphthalene-1-sulfonylamino-octyl-amide) | ||||||
Components | Cytochrome P450-cam | ||||||
Keywords | OXIDOREDUCTASE / MONOOXYGENASE / ELECTRON TRANSFER / ENERGY TRANSFER / SUBSTRATE-BINDING / DANSYL / ADAMANTANE / Adamantane-1-carboxylic acid [4-(5-dimethylamino-naphthalene-1-sulfonylamino)-octyl]-amide / CHANNEL | ||||||
Function / homology | Function and homology information camphor 5-monooxygenase / camphor 5-monooxygenase activity / (+)-camphor catabolic process / iron ion binding / heme binding / cytoplasm Similarity search - Function | ||||||
Biological species | Pseudomonas putida (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Dunn, A.R. / Hays, A.M. / Goodin, D.B. / Stout, C.D. / Chiu, R. / Winkler, J.R. / Gray, H.B. | ||||||
Citation | Journal: J.AM.CHEM.SOC. / Year: 2002 Title: Fluorescent probes for cytochrome P450 structural characterization and inhibitor screening Authors: Dunn, A.R. / Hays, A.M. / Goodin, D.B. / Stout, C.D. / Chiu, R. / Winkler, J.R. / Gray, H.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1lwl.cif.gz | 101.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lwl.ent.gz | 76.2 KB | Display | PDB format |
PDBx/mmJSON format | 1lwl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1lwl_validation.pdf.gz | 536.3 KB | Display | wwPDB validaton report |
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Full document | 1lwl_full_validation.pdf.gz | 547.6 KB | Display | |
Data in XML | 1lwl_validation.xml.gz | 11.3 KB | Display | |
Data in CIF | 1lwl_validation.cif.gz | 18 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lw/1lwl ftp://data.pdbj.org/pub/pdb/validation_reports/lw/1lwl | HTTPS FTP |
-Related structure data
Related structure data | 2cppS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 46961.359 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas putida (bacteria) / Plasmid: PUS200 / Production host: Escherichia coli (E. coli) / Strain (production host): TBY / References: UniProt: P00183, camphor 5-monooxygenase |
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#2: Chemical | ChemComp-HEM / |
#3: Chemical | ChemComp-DSO / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.28 % | ||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: Citrate, PEG, KCl, DTT, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ | ||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 105 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 16, 2002 / Details: osmic confocal mirrors |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→20 Å / Num. all: 21045 / Num. obs: 21045 / % possible obs: 93.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): -3 / Redundancy: 5.2 % / Biso Wilson estimate: 26.2 Å2 / Rsym value: 0.102 / Net I/σ(I): 13.9 |
Reflection shell | Resolution: 2.2→2.3 Å / Mean I/σ(I) obs: 2.5 / Rsym value: 0.266 / % possible all: 63.8 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. measured all: 115720 / Rmerge(I) obs: 0.102 |
Reflection shell | *PLUS % possible obs: 63.8 % / Rmerge(I) obs: 0.266 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2CPP Resolution: 2.2→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.2→20 Å
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LS refinement shell | Resolution: 2.2→2.3 Å
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Refinement | *PLUS Lowest resolution: 20 Å / % reflection Rfree: 4.8 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 2.3 Å / Rfactor Rfree: 0.33 / Rfactor Rwork: 0.285 |